# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:01:44 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-(1,3-dihydro-2H-isoindol-2-ylcarbonyl)-6-(1-methylethyl)benzene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1cc(c(O)cc1O)C(=O)N2Cc3ccccc3C2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VHD  VHD  4-(1,3-dihydro-2H-isoindol-2-ylcarbonyl)-6-(1-methylethyl)benzene-1,3-diol  ligand  41  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VHD
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VHD  C1    C  CH3   0  -0.635   2.1660   3.3495   0.1504
 VHD  C2    C  CH1   0  -0.336   3.1455   2.2836   0.6418
 VHD  C3    C  CH3   0  -0.637   3.3189   2.3452   2.1590
 VHD  C4    C  CR6   0   0.031   2.7246   0.9018   0.1826
 VHD  C5    C  CR16  0  -0.295   1.5261   0.3650   0.6396
 VHD  C6    C  CR6   0  -0.169   1.0560  -0.8835   0.2648
 VHD  C7    C  C     0   0.521  -0.2032  -1.4340   0.8495
 VHD  O8    O  O     0  -0.492  -0.1933  -2.3988   1.6032
 VHD  N9    N  NR5   0  -0.494  -1.3386  -0.7987   0.5195
 VHD  C10   C  CH2   0  -0.279  -2.6226  -1.2500   1.0468
 VHD  C11   C  CR56  0   0.044  -3.5979  -0.3979   0.2976
 VHD  C12   C  CR16  0  -0.314  -4.9808  -0.3864   0.3853
 VHD  C13   C  CR16  0  -0.256  -5.6928   0.4957  -0.4186
 VHD  C14   C  CR16  0  -0.256  -5.0280   1.3496  -1.2945
 VHD  C15   C  CR16  0  -0.311  -3.6411   1.3345  -1.3780
 VHD  C16   C  CR56  0   0.051  -2.9369   0.4526  -0.5737
 VHD  C17   C  CH2   0  -0.267  -1.4555   0.2642  -0.4782
 VHD  C18   C  CR6   0   0.346   1.8202  -1.6464  -0.6200
 VHD  O19   O  OH1   0  -0.622   1.3407  -2.8475  -0.9884
 VHD  C20   C  CR16  0  -0.474   3.0168  -1.1413  -1.1022
 VHD  C21   C  CR6   0   0.299   3.4697   0.1161  -0.7051
 VHD  O22   O  OH1   0  -0.625   4.6467   0.5014  -1.2353
 VHD  H11C  H  HCH3  0   0.232   2.4846   4.3422   0.4712
 VHD  H12C  H  HCH3  0   0.234   2.0967   3.3520  -0.9376
 VHD  H13C  H  HCH3  0   0.221   1.1628   3.1821   0.5476
 VHD  H2    H  HCH1  0   0.224   4.1203   2.5404   0.2144
 VHD  H31C  H  HCH3  0   0.223   2.3811   2.1395   2.6776
 VHD  H32C  H  HCH3  0   0.234   4.0567   1.6201   2.5031
 VHD  H33C  H  HCH3  0   0.233   3.6526   3.3378   2.4646
 VHD  H5    H  HCR6  0   0.263   0.9285   0.9495   1.3304
 VHD  H101  H  HCH2  0   0.261  -2.7739  -2.3164   0.8578
 VHD  H102  H  HCH2  0   0.261  -2.6829  -1.1010   2.1289
 VHD  H171  H  HCH2  0   0.261  -0.9585   1.1836  -0.1586
 VHD  H172  H  HCH2  0   0.267  -1.0108  -0.0315  -1.4320
 VHD  H12   H  HCR6  0   0.255  -5.5014  -1.0487   1.0659
 VHD  H13   H  HCR6  0   0.258  -6.7735   0.5198  -0.3627
 VHD  H14   H  HCR6  0   0.258  -5.5970   2.0312  -1.9133
 VHD  H15   H  HCR6  0   0.254  -3.1243   2.0005  -2.0581
 VHD  H19   H  HOH1  0   0.479   1.9301  -3.2660  -1.6261
 VHD  H20   H  HCR6  0   0.277   3.6141  -1.7192  -1.7993
 VHD  H22   H  HOH1  0   0.473   4.9038   1.3723  -0.9142

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VHD  C1   C2    single    1.529  0.020  1.529
 VHD  C2   C3    single    1.528  0.020  1.528
 VHD  C2   C4    single    1.516  0.020  1.516
 VHD  C4   C5    aromatic  1.390  0.020  1.390
 VHD  C4   C21   aromatic  1.400  0.020  1.400
 VHD  C5   C6    aromatic  1.386  0.020  1.386
 VHD  C6   C7    single    1.493  0.020  1.493
 VHD  C6   C18   aromatic  1.396  0.020  1.396
 VHD  C7   O8    double    1.224  0.020  1.224
 VHD  C7   N9    single    1.342  0.020  1.342
 VHD  N9   C10   single    1.460  0.020  1.460
 VHD  N9   C17   single    1.462  0.020  1.462
 VHD  C10  C11   single    1.496  0.020  1.496
 VHD  C11  C12   aromatic  1.386  0.020  1.386
 VHD  C11  C16   aromatic  1.385  0.020  1.385
 VHD  C12  C13   aromatic  1.390  0.020  1.390
 VHD  C13  C14   aromatic  1.392  0.020  1.392
 VHD  C14  C15   aromatic  1.390  0.020  1.390
 VHD  C15  C16   aromatic  1.386  0.020  1.386
 VHD  C16  C17   single    1.496  0.020  1.496
 VHD  C18  O19   single    1.345  0.020  1.345
 VHD  C18  C20   aromatic  1.385  0.020  1.385
 VHD  C20  C21   aromatic  1.394  0.020  1.394
 VHD  C21  O22   single    1.347  0.020  1.347
 VHD  C1   H11C  single    0.970  0.020  1.090
 VHD  C1   H12C  single    0.970  0.020  1.090
 VHD  C1   H13C  single    0.970  0.020  1.090
 VHD  C2   H2    single    0.970  0.020  1.090
 VHD  C3   H31C  single    0.970  0.020  1.090
 VHD  C3   H32C  single    0.970  0.020  1.090
 VHD  C3   H33C  single    0.970  0.020  1.090
 VHD  C5   H5    single    0.930  0.020  1.080
 VHD  C10  H101  single    0.970  0.020  1.090
 VHD  C10  H102  single    0.970  0.020  1.090
 VHD  C17  H171  single    0.970  0.020  1.090
 VHD  C17  H172  single    0.970  0.020  1.090
 VHD  C12  H12   single    0.930  0.020  1.080
 VHD  C13  H13   single    0.930  0.020  1.080
 VHD  C14  H14   single    0.930  0.020  1.080
 VHD  C15  H15   single    0.930  0.020  1.080
 VHD  O19  H19   single    0.850  0.020  0.980
 VHD  C20  H20   single    0.930  0.020  1.080
 VHD  O22  H22   single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VHD  H13C  C1   H12C  107.76  3.000
 VHD  H13C  C1   H11C  107.50  3.000
 VHD  H12C  C1   H11C  108.06  3.000
 VHD  H13C  C1   C2    111.40  3.000
 VHD  H12C  C1   C2    111.29  3.000
 VHD  H11C  C1   C2    110.66  3.000
 VHD  H2    C2   C4    110.05  3.000
 VHD  H2    C2   C3    106.09  3.000
 VHD  C4    C2   C3    111.65  3.000
 VHD  H2    C2   C1    106.34  3.000
 VHD  C4    C2   C1    111.12  3.000
 VHD  C3    C2   C1    111.32  3.000
 VHD  H33C  C3   H32C  108.04  3.000
 VHD  H33C  C3   H31C  107.54  3.000
 VHD  H32C  C3   H31C  107.84  3.000
 VHD  H33C  C3   C2    110.45  3.000
 VHD  H32C  C3   C2    111.30  3.000
 VHD  H31C  C3   C2    111.51  3.000
 VHD  C21   C4   C5    116.77  3.000
 VHD  C21   C4   C2    123.77  3.000
 VHD  C5    C4   C2    119.46  3.000
 VHD  H5    C5   C6    118.10  3.000
 VHD  H5    C5   C4    118.44  3.000
 VHD  C6    C5   C4    123.46  3.000
 VHD  C18   C6   C7    120.55  3.000
 VHD  C18   C6   C5    118.56  3.000
 VHD  C7    C6   C5    120.81  3.000
 VHD  N9    C7   O8    122.09  3.000
 VHD  N9    C7   C6    116.26  3.000
 VHD  O8    C7   C6    121.65  3.000
 VHD  C17   N9   C10   113.63  3.000
 VHD  C17   N9   C7    125.41  3.000
 VHD  C10   N9   C7    120.59  3.000
 VHD  H102  C10  H101  107.23  3.000
 VHD  H102  C10  C11   112.45  3.000
 VHD  H101  C10  C11   112.25  3.000
 VHD  H102  C10  N9    111.33  3.000
 VHD  H101  C10  N9    111.15  3.000
 VHD  C11   C10  N9    102.50  3.000
 VHD  C16   C11  C12   120.72  3.000
 VHD  C16   C11  C10   110.70  3.000
 VHD  C12   C11  C10   128.57  3.000
 VHD  H12   C12  C13   120.36  3.000
 VHD  H12   C12  C11   120.96  3.000
 VHD  C13   C12  C11   118.68  3.000
 VHD  H13   C13  C14   119.71  3.000
 VHD  H13   C13  C12   119.72  3.000
 VHD  C14   C13  C12   120.57  3.000
 VHD  H14   C14  C15   119.82  3.000
 VHD  H14   C14  C13   119.66  3.000
 VHD  C15   C14  C13   120.51  3.000
 VHD  H15   C15  C16   120.88  3.000
 VHD  H15   C15  C14   120.48  3.000
 VHD  C16   C15  C14   118.64  3.000
 VHD  C17   C16  C15   128.33  3.000
 VHD  C17   C16  C11   110.79  3.000
 VHD  C15   C16  C11   120.88  3.000
 VHD  H172  C17  H171  107.32  3.000
 VHD  H172  C17  C16   112.40  3.000
 VHD  H171  C17  C16   111.28  3.000
 VHD  H172  C17  N9    111.48  3.000
 VHD  H171  C17  N9    112.06  3.000
 VHD  C16   C17  N9    102.37  3.000
 VHD  C20   C18  O19   122.56  3.000
 VHD  C20   C18  C6    119.61  3.000
 VHD  O19   C18  C6    117.81  3.000
 VHD  H19   O19  C18   110.55  3.000
 VHD  H20   C20  C21   118.99  3.000
 VHD  H20   C20  C18   120.33  3.000
 VHD  C21   C20  C18   120.68  3.000
 VHD  O22   C21  C20   115.44  3.000
 VHD  O22   C21  C4    123.64  3.000
 VHD  C20   C21  C4    120.92  3.000
 VHD  H22   O22  C21   111.14  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VHD  CONST_01  C18   C6   C5   C4      0.00   0.0  0
 VHD  CONST_02  C18   C20  C21  C4      0.00   0.0  0
 VHD  CONST_03  C20   C21  C4   C5      0.00   0.0  0
 VHD  CONST_04  C20   C18  C6   C5      0.00   0.0  0
 VHD  CONST_05  C21   C4   C5   C6      0.00   0.0  0
 VHD  CONST_06  C21   C20  C18  C6      0.00   0.0  0
 VHD  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 VHD  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 VHD  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 VHD  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 VHD  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 VHD  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 VHD  CONST_13  C6    C5   C4   C2    180.00   0.0  0
 VHD  CONST_14  C20   C21  C4   C2    180.00   0.0  0
 VHD  CONST_15  C7    C6   C5   C4    180.00   0.0  0
 VHD  CONST_16  O22   C21  C4   C5    180.00   0.0  0
 VHD  CONST_17  O19   C18  C6   C5    180.00   0.0  0
 VHD  CONST_18  C20   C18  C6   C7    180.00   0.0  0
 VHD  CONST_19  O22   C21  C20  C18   180.00   0.0  0
 VHD  CONST_20  C21   C20  C18  O19   180.00   0.0  0
 VHD  CONST_21  C10   N9   C7   C6    180.00   0.0  0
 VHD  CONST_22  C17   N9   C7   C6      0.00   0.0  0
 VHD  CONST_23  H20   C20  C21  C4    180.00   0.0  0
 VHD  CONST_24  H12   C12  C11  C10     0.00   0.0  0
 VHD  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 VHD  CONST_26  H15   C15  C16  C11   180.00   0.0  0
 VHD  CONST_27  H14   C14  C13  C12   180.00   0.0  0
 VHD  CONST_28  H5    C5   C6   C18   180.00   0.0  0
 VHD  CONST_29  C10   N9   C7   O8      0.00   0.0  0
 VHD  CONST_30  C17   N9   C7   O8    180.00   0.0  0
 VHD  Var_01    C12   C11  C10  N9    179.94  30.0  1
 VHD  Var_02    C11   C16  C17  N9      0.99  30.0  1
 VHD  Var_03    C16   C17  N9   C10    -0.91  30.0  1
 VHD  Var_04    C17   N9   C10  C11     0.51  30.0  1
 VHD  Var_05    N9    C7   C6   C5     67.11  30.0  2
 VHD  Var_06    C5    C4   C2   C1    -64.11  30.0  2
 VHD  Var_07    H11C  C1   C2   C4   -179.09  30.0  3
 VHD  Var_08    H31C  C3   C2   C4    -62.30  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VHD  plan-1  C2   0.020
 VHD  plan-1  C4   0.020
 VHD  plan-1  C5   0.020
 VHD  plan-1  C6   0.020
 VHD  plan-1  C7   0.020
 VHD  plan-1  C18  0.020
 VHD  plan-1  O19  0.020
 VHD  plan-1  C20  0.020
 VHD  plan-1  C21  0.020
 VHD  plan-1  O22  0.020
 VHD  plan-1  H5   0.020
 VHD  plan-1  H20  0.020
 VHD  plan-2  C10  0.020
 VHD  plan-2  C11  0.020
 VHD  plan-2  C12  0.020
 VHD  plan-2  C13  0.020
 VHD  plan-2  C14  0.020
 VHD  plan-2  C15  0.020
 VHD  plan-2  C16  0.020
 VHD  plan-2  C17  0.020
 VHD  plan-2  H12  0.020
 VHD  plan-2  H13  0.020
 VHD  plan-2  H14  0.020
 VHD  plan-2  H15  0.020
 VHD  plan-3  C6   0.020
 VHD  plan-3  C7   0.020
 VHD  plan-3  O8   0.020
 VHD  plan-3  N9   0.020
 VHD  plan-3  C10  0.020
 VHD  plan-3  C17  0.020

